Question: How to perform FPKM on raw reads in R
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gravatar for manish20072013
2.7 years ago by
manish200720130 wrote:

How I perform fpkm on a file containing the raw reads of two samples and each sample have three replicates? I want to do the analysis in R.

sequencing rna-seq fpkm R • 4.0k views
ADD COMMENTlink modified 10 months ago by Ahmed Alhendi30 • written 2.7 years ago by manish200720130
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gravatar for Istvan Albert
2.7 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

See the blog post "What the FPKM" by Harold Pimentel that also provides R code:

https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Istvan Albert ♦♦ 82k
1
gravatar for Ahmed Alhendi
10 months ago by
University of Southampton, UK
Ahmed Alhendi30 wrote:

Try countToFPKM package. This package provides an easy to use function to convert the read count matrix into FPKM values normalised by library size and feature effective length. It also provides the user with a reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.; following the equation:

enter image description here.

The fpkm() function requires three inputs to return FPKM as numeric matrix normalized by library size and feature length:

  • counts A numeric matrix of raw feature counts.
  • featureLength A numeric vector with feature lengths that can be obtained using biomaRt.
  • meanFragmentLength A numeric vector with mean fragment lengths, which can be calculate with
    Picard using CollectInsertSizeMetrics.

Also see https://github.com/AAlhendi1707/countToFPKM

ADD COMMENTlink written 10 months ago by Ahmed Alhendi30
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